<<<<<<< HEAD
Sample Homogenization - C.gigas Lifestage Carryover Samples Using TriZol and Bullet Blender
2025
Bullet Blender
homogenization
TriZol
Crassostrea gigas
Pacific oyster
Magallana gigas
May 12, 2025
=======
<<<<<<< HEAD
DNA RNA Isolation and Quantification - G.macrocephalus Blood Using Bullet Blender and Zymo Quick DNA RNA MiniPrep
2025
Bullet Blender
Pacific cod
Gadus macrocephalus
blood
DNA isolation
RNA isolation
DNA quantification
RNA quantification
Qubit
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DIAMOND BLAST Database - NCBI NR Database and Taxonomy Nodes on Raven
2025
DIAMOND
BLAST
Raven
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA RNA Isolation and Quantification - G.macrocephalus Blood Using Bullet Blender and Zymo Quick DNA RNA MiniPrep
2025
Bullet Blender
Pacific cod
Gadus macrocephalus
blood
DNA isolation
RNA isolation
DNA quantification
RNA quantification
Qubit
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA RNA Isolation and Quantification - G.macrocephalus Blood Using Bullet Blender and Zymo Quick DNA RNA MiniPrep Plus Kit
2025
Bullet Blender
Pacific cod
Gadus macrocephalus
blood
DNA isolation
RNA isolation
DNA quantification
RNA quantification
Qubit
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Taxonomy Assignment - Yellow Island 2018 eDNA Samples Using QIIME 2
2025
taxonomy
Yellow Island
eDNA
QIIME 2
=======
Trimming - Yellow Island eDNA FastQs Using Fastp FastQC and MultiQC
2025
eDNA
Yellow Island
fastp
trimming
FastQC
MultiQC
project-eDNA-yellow
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - Yellow Island eDNA Project
2025
eDNA
Yellow Island
FastQC
MultiQC
project-eDNA-yellow
Trimming - Yellow Island eDNA FastQs Using Fastp FastQC and MultiQC
2025
eDNA
Yellow Island
fastp
trimming
FastQC
MultiQC
project-eDNA-yellow
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA RNA Isolation and Quantification - G.macrocephalus Blood Using Bullet Blender and Zymo Quick DNA RNA MiniPrep Plus Kit
2025
Bullet Blender
Pacific cod
Gadus macrocephalus
blood
DNA isolation
RNA isolation
DNA quantification
RNA quantification
Qubit
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA RNA Isolation and Quantification - G.macrocephalus Blood Using Bullet Blender and Zymo Quick DNA RNA MiniPrep Plus Kit
2025
Bullet Blender
Pacific cod
Gadus macrocephalus
blood
DNA isolation
RNA isolation
DNA quantification
RNA quantification
Qubit
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Samples Submitted - S.namaycush Live gDNA to Angie Schmoldt at UW-Milwaukee
2025
Samples Submitted
lake trout
gDNA
liver
Salvelinus namaycush
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Computer Management - Install Synology Expansion Unit RX1217 for Gannet
2025
Computer Management
Synology
RX1217
expansion
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA and RNA Isolations and Quantification - G.macrocephalus Blood Using Zymo Quick-RNA RNA MiniPrep Plus Kit
2025
Gadus macrocephalus
Pacific cod
blood
DNA isolation
RNA isolation
Qubit
DNA quantification
RNA quantification
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA Concentration - S.namaycush DNA from 20250220 Using SpeedVac
2025
lake trout
Salvelinus namaycush
SpeedVac
=======
Alignment - P.tuahiniensis RNA-seq Data from E5 timeseries_molecular Project Using Hisat2
2025
Pocillopora tuahiniensis
E5
coral
Hisat2
alignment
RNAseq
Stringtie
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - P.evermanni Using Hisat2 on Raven
2025
Porites evermanni
E5
coral
Hisat2
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - P.tuahiniensis Using Hisat2 on Raven
2025
Pocillopora tuahiniensis
E5
coral
Hisat2
Alignment - P.tuahiniensis RNA-seq Data from E5 timeseries_molecular Project Using Hisat2
2025
Pocillopora tuahiniensis
E5
coral
Hisat2
alignment
RNAseq
Stringtie
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Alignment - P.evermanni RNA-seq Data from E5 timeseries_molecular Project Using Hisat2
2025
Porites evermanni
E5
coral
Hisat2
alignment
RNAseq
Stringtie
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Agarose Gel - S.namaycush Liver gDNA from 20250220
2025
agarose gel
gDNA
liver
Lake trout
Salvelinus namaycush
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming - P.evermanni RNA-seq Trimming and QC with fastp FastQC and MultiQC for E5 timeseries_molecular Project
2025
Porites evermanni
E5
trimming
fastp
FastQC
MultiQC
RNAseq
timeseries_molecular
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming - P.tuahiniensis RNA-seq Trimming and QC with fastp FastQC and MultiQC for E5 timeseries_molecular Project
2025
Pocillopora tuahiniensis
E5
trimming
fastp
FastQC
MultiQC
RNAseq
timeseries_molecular
=======
DNA Isolation and Quantification - S.namaycush Liver
2025
lake trout
Salvelinus namaycush
DNA isolation
Qubit
DNA quantification
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - P.evermanni RNA-seq Data for timeseries_molecular Project
2025
Porites evermanni
E5
FastQC
MultiQC
RNAseq
timeseries_molecular
DNA Isolation and Quantification - S.namaycush Liver
2025
lake trout
Salvelinus namaycush
DNA isolation
Qubit
DNA quantification
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - P.tuahiniensis RNA-seq Data for timeseries_molecular Project
2025
Pocillopora tuahiniensis
E5
FastQC
MultiQC
timeseries_molecular
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming - P.evermanni WGBS Trimming and QC with fastp FastQC and MultiQC for E5 timeseries_molecular Project
2025
Porites evermanni
E5
WGBS
bisulfite sequencing
FastQC
MultiQC
fastp
trimming
timeseries_molecular
coral
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming - P.tuahiniensis WGBS Trimming and QC with fastp FastQC and MultiQC for E5 timeseries_molecular Project
2025
Porites tuahiniensis
E5
WGBS
bisulfite sequencing
FastQC
MultiQC
fastp
trimming
timeseries_molecular
coral
=======
FastQC MultiQC - P.evermanni Raw WGBS Renaming and FastQC MultiQC E5 timeseries_molecular Project
2025
Porites evermanni
E5
WGBS
bisulfite sequencing
FastQC
MultiQC
timeseries_molecular
coral
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - P.tuahiniensis Raw WGBS Renaming and FastQC MultiQC timeseries_molecular Project
2025
Pocillopora tuahiniensis
E5
WGBS
bisulfite sequencing
FastQC
MultiQC
timeseries_molecular
coral
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - P.evermanni Raw WGBS Renaming and FastQC MultiQC E5 timeseries_molecular Project
2025
Porites evermanni
E5
WGBS
bisulfite sequencing
FastQC
MultiQC
timeseries_molecular
coral
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - P.evermanni WGBS E5 Deep Dive Expression
2025
Porites evermanni
E5
deep-dive-expression
FastQC
MultiQC
WGBS
BS-seq
bisulfite sequencing
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - P.tuahiniensis WGBS E5 Deep Dive Expression
2025
Pocillopora tuahiniensis
E5
deep-dive-expression
FastQC
MultiQC
WGBS
BS-seq
bisulfite sequencing
FastQC MultiQC - A.pulchra WGBS E5 Deep Dive Expression
2025
Acropora pulchra
E5
deep-dive-expression
FastQC
MultiQC
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - E5 Coral WGBS from Genohub Project 2216545 Using Rclone on Owl
2025
E5
coral
WGBS
BS-seq
bisulfite sequencing
Genohub
2216545
Data Received
rclone
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Differential Expression - R.philippinarum miRNAs Using DEseq2
2025
Ruditapes philippinarum
Manila clam
DEseq2
sRNA-seq
miRNA
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Computer Management - Fix Most of Raven Boot Issues
2025
raven
Computer Management
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Bisulfite Genome - P.tuahiniensis BS Genome Using Bismark
2025
Pocillopora tuahiniensis
bismark
bisulfite
coral
E5
timeseries_molecular
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Bisulfite Genome - P.evermanni BS Genome Using Bismark
2025
Porites evermanni
E5
timeseries_molecular
bismark
bisulfite genome
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Primer Design - C.gigas Alternative Oxidase AOX Variants Using Primer3
2025
Crassotrea gigas
Pacific oyster
Primer3
EMBOSS
PrimerSearch
Magallana gigas
primers
AOX
alternative oxidase
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - Reformat P.tuahiniensis GFF to Valid GFF3 Using awk genometools and AGAT
2025
GFF
genometools
E5
timeseries_molecular
Porites tuahiniensis
coral
AGAT
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - Reformat P.evermanni GFF to Valid GFF3 Using awk genometools and AGAT
2025
GFF
genometools
E5
timeseries_molecular
Porites evermanni
coral
AGAT
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Bismark Alignments - A.pulchra Trimmed Reads Using Bismark on Hyak
2025
Bismark
Acropora pulchra
coral
timeseries_molecular
E5
klone
hyak
alignment
WGBS
=======
Bisulfite Genome - A.pulchra BS Genome Using Bismark
2025
Acropora pulchra
bismark
bisulfite
coral
E5
timeseries_molecular
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming - A.pulchra WGBS with fastp FastQC and MultiQC on Raven
2025
Acopora pulchra
WGBS
trimming
fastp
FastQC
MultiQC
Raven
Bisulfite Genome - A.pulchra BS Genome Using Bismark
2025
Acropora pulchra
bismark
bisulfite
coral
E5
timeseries_molecular
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC MultiQC - A.pulchra WGBS E5 Timeseries
2024
E5
timeseries_molecular
WGBS
Acropora pulchra
FastQC
MultiQC
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - Coral E5 WGBS Time Series from Azenta Project 30-1067895835
2024
E5
30-1067895835
WGBS
BS-seq
bisulfite
Data Received
timeseries_molecular
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - S.pacificus WGBS Data from Azenta Project 30-1067895835
2024
WGBS
BS-seq
Data Received
bisulfite
30-1067895835
Somniosus pacificus
sleeper shark
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - G.macrocephalus WGBS Data from Azenta Project 30-1067895835
2024
WGBS
BS-seq
Data Received
bisulfite
30-1067895835
Pacific cod
Gadus macrocephalus
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR Analysis - C.gigas Lifestages Carryover
2024
Crassostrea gigas
Pacific oyster
qPCR
project-gigas-carryover
lifestage_carryover
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - C.gigas Lifestage Carryover VIPERIN
2024
Crassostrea gigas
Pacific oyster
SsoFast
CFX Connect
CFX96
project-gigas-carryover
VIPERIN
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCRs - C.gigas Lifestage Carryover citrate synthase DNMT1 HSP70 and HSP90
2024
Crassostrea gigas
Pacific oyster
SsoFast
CFX Connect
CFX96
project-gigas-carryover
citrate synthase
DNMT1
HSP70
HSP90
=======
Data Received - Coral E5 sRNA-seq Time Series Azenta Project 30-1069297013
2024
coral
E5
sRNA-seq
timeseries_molecular
Data Received
30-1069297013
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
miRNA Identification - R.phillipinarum sRNA-seq Using ShortStack and miRBase Mature miRNAs
2024
Ruditapes phillipinarum
Manila clam
sRNA-seq
miRNA
project-clam-oa
ShortStack
miRBase
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCRs - C.gigas Lifestage Carryover GAPDH ATP_synthase and cGAS
2024
Crassostrea gigas
Pacific oyster
GAPDH
ATP synthase
cGAS
SsoFast
CFX Connect
CFX96
project-gigas-carryover
Data Received - Coral E5 sRNA-seq Time Series Azenta Project 30-1069297013
2024
coral
E5
sRNA-seq
timeseries_molecular
Data Received
30-1069297013
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming and Merging - R.philippinarum sRNA-seq Data Using fastp FastQC and MultiQC
2024
Ruditapes philippinarum
Manila clam
project-clam-oa
sRNA-seq
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQ Concatentation and QC - R.philippinarum sRNA-seq Data Using FastQC and MultiQC
2024
Manila clam
Ruditapes philippinarum
30-1035633055
30-1035633055-TS01
project-clam-oa
FastQC
MultiQC
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Methylation Extraction - C.virginica CEASMALLR WGBS Using Bismark
2024
Crassostrea virginica
Eastern oyster
ceasmallr
wgbs
BS-seq
Bismark
methylation extraction
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Deduplication - C.virginica CEASMALLR WGBS Using Bismark
2024
Crassostrea virginica
Eastern oyster
ceasmallr
Bismark
WGBS
BS-seq
deduplication
=======
Alignment - C.virginica CEASMALLR WGBS Using Bismark on Klone Array
2024
trimming
Crassostrea virginica
Eastern oyster
ceasmallr
WGBS
BS-seq
Klone
Bismark
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Computer Management - Replace Failed Hard Drive on Gannet
2024
Gannet
HDD
Computer Management
Alignment - C.virginica CEASMALLR WGBS Using Bismark on Klone Array
2024
trimming
Crassostrea virginica
Eastern oyster
ceasmallr
WGBS
BS-seq
Klone
Bismark
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming and QC - C.virginica CEASMALLR FastQs Using fastp BBTools and FastQC-MultiQC
2024
trimming
FastQC
fastp
BBTools
MultiQC
Crassostrea virginica
WGBS
BS-seq
bisulfite
Eastern oyster
ceasmallr
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Taxonomic Classification - Trinity Assembly of Unmapped P.helianthoides RNA-seq Using DIAMOND BLASTx and MEGAN6 on Mox
2024
DIAMOND
BLASTx
MEGAN6
Pycnopodia helianthoides
sunflower sea star
Mox
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQ QC - M.trossulus WGBS from Psomagen Using FastQC and MultiQC
2024
Mytilus trossulus
WGBS
Psomagen
FastQC
MultiQC
mussel
project-mytilus-methylation
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming and QC - M.trossulus WGBS Using fastp and FastQC-MultiQC
2024
Mytilus trossulus
WGBS
fastp
FastQC
MultiQC
bay mussel
project-mytilus-methylation
trimming
=======
Data Wrangling - GO to GOslims for Graces Pycnopodia helianthoides Project from Trinity Assembly Genes
2024
GO
gene ontology
GOslim
Pycnopodia helianthoides
Trinity
Sunflower sea star
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - GO to GOslims for Graces Dermasterias imbricata Project from Trinity Assembly Genes
2024
Dermasterias imbricata
GO
GOslim
gene ontology
Trinity
Leather star
Data Wrangling - GO to GOslims for Graces Pycnopodia helianthoides Project from Trinity Assembly Genes
2024
GO
gene ontology
GOslim
Pycnopodia helianthoides
Trinity
Sunflower sea star
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Sequencing Read Taxonomic Classification - Unmapped P.helanthoides RNA-seq Using DIAMOND-BLASTx and MEGAN6 on Mox
2024
MEGAN6
RNAseq
DIAMOND
BLASTx
Pycnopodia helianthoides
sunflower sea star
Mox
=======
Data Received - Mytilus trossulus WGBS Data from Psomagen
2024
Mytilus trossulus
bay mussel
WGBS
Psomagen
AN00021156
BS-seq
bisulfite sequencing
Data Received
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - November 2024
2024
Daily Bits
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - Manila clam Supplemental sRNA-seq Data from Azenta
2024
sRNA-seq
Manila clam
Ruditapes philippinarum
30-1035633055
30-1035633055-TS01
Data Received
Data Received - Mytilus trossulus WGBS Data from Psomagen
2024
Mytilus trossulus
bay mussel
WGBS
Psomagen
AN00021156
BS-seq
bisulfite sequencing
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - Get GOslims from GO IDs for Graces Pycnopodia helianthoides Project
2024
Pycnopodia helianthoides
sunflower sea star
gene ontology
GO
GOslim
data wrangling
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA Isolation Quantification and Gel - Lake Trout Liver Samples
2024
DNA isolation
Qubit
DNA quantification
agarose gel
lake trout
Salvelinus namaycush
liver
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Reverse Transcription - C.gigas Lifestage Carryover RNA
2024
reverse transcription
cDNA
GoScript
Crassostrea gigas
Pacific oyster
RNA
project-gigas-carryover
lifestage_carryover
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Computer Management - Configure 16TB OWC ThunderBlade X8 External HDD on Raven
2024
Computer Management
HDD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
PCR - Lake Trout C1q Primers with Bisulfite-treated gDNA
2024
C1q
Lake trout
Salvelinus namaycush
PCR
bisulfite
gDNA
liver
gel
=======
Data Wrangling - Generate GTF from A.pulchra Genome GFF Using gffread
2024
coral
Acropora pulchra
genome
GFF
GTF
gffread
E5
timeseries_molecular
RNA-seq Alignment - A.pulchra RNA-seq Alignments Using HISAT2 and StringTie for Azenta Project 30-1047560508
2024
30-1047560508
RNA-seq
E5
timeseries_molecular
HISAT2
StringTie
alignment
Acropora pulchra
coral
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - A.pulchra Genome Using HISAT2
2024
coral
Acropora pulchra
HISAT2
E5
timeseries_molecular
RNA-seq Alignment - A.pulchra RNA-seq Alignments Using HISAT2 and StringTie for Azenta Project 30-1047560508
2024
30-1047560508
RNA-seq
E5
timeseries_molecular
HISAT2
StringTie
alignment
Acropora pulchra
coral
Data Wrangling - Generate GTF from A.pulchra Genome GFF Using gffread
2024
coral
Acropora pulchra
genome
GFF
GTF
gffread
E5
timeseries_molecular
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQC Trimming and QC - A.pulchra RNA-seq from Azenta Project 30-1047560508 Using fastp
2024
RNA-seq
30-1047560508
Azenta
coral
Acropora pulchra
fastp
FastQC
MultiQC
trimming
E5
timeseries_molecular
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQ QC - A.pulchra RNA-seq from Azenta Project 30-1047560508
2024
RNA-seq
30-1047560508
Azenta
coral
Acropora pulchra
FastQC
MultiQC
timeseries_molecular
E5
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - R.philippinarum (Manilla clam) sRNA-seq Data from Azenta Project 30-1035633055
2024
Data Received
sRNA-seq
30-1035633055
Ruditapes philippinarum
Manila clam
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - October 2024
2024
Daily Bits
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - E5 Coral Time Series RNA-seq Azenta Project 30-1047560508
2024
E5
coral
RNA-seq
30-1047560508
Azenta
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Agarose Gel - gDNA Integrity Check of Lake Trout Liver gDNA from 20240712
2024
agarose gel
gDNA
Lake trout
liver
Salvelinus namaycush
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
PCR - Lake Trout C1Q with Liver gDNA
2024
PCR
Lake trout
C1q
CFX Connect
EpiMark Hot Start Taq
gDNA
liver
Salvelinus namaycush
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Primer Design - Lake Trout C1q Gene Sequencing Primers Using Primer3
2024
C1q
lake trout
Salvelinus namaycush
Primer3
primer design
EMBOSS
pyfaidx
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Bisulfite PCR - Second Primer Annealing Gradient Test with Lake Trout Bisulfite-treated DNA
2024
bisulfite
BS-PCR
PCR
DNA
Lake troute
Salvelinus namaycush
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - G.macrocephalus Supplemental RNA-seq Data from Azenta Project 30-943133806
Data Received
2024
Gadus macrocephalus
Pacific cod
RNA-seq
Azenta
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - September 2024
Daily Bits
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA and RNA Isolations - Gadus macrocephalus Blood
2024
DNA isolation
RNA isolation
Gadus macrocephalus
Pacific cod
blood
Zymo Quick-DNA/RNA Miniprep
Qubit 3.0
Qubit DNA BR Assay
Qubit RNA HS Assay
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Bisulfite PCR - Testing Primer Annealing Gradient with Lake Trout Bisulfite-treated DNA
2024
BS-PCR
bisulfite
PCR
DNA
Lake trout
Salvelinus namaycush
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Bisulfite Conversion - Lake Trout gDNA Using EZ DNA Methylation Lightning Kit
2024
lake trout
Salvelinus namaycush
bisulfite
EZ DNA Methylation Lightning Kit
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - August 2024
2024
Daily Bits
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Primer Design - Lake Trout C1q Gene Bisulfite Sequencing Primers Using Primer3
2024
C1q
lake trout
Salvelinus namaycush
Primer3
primer design
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Samples Submitted - Macs Manilla Clam Egg Samples for sRNA-seq at Azenta
2024
Samples Submitted
Azenta
sRNA-seq
Manila clam
Lajonkairia lajonkairii
Ruditapes philippinarum
eggs
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA Isolation Quantification and Integrity Assessment - Pacific Cod Blood Samples Test
2024
Pacific cod
Gadus macrocephalus
DNA isolation
DNA quantification
Qubit
DNA BR Assay
agarose gel
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA Isolation and Quantification - Pacific Cod Blood
2024
Pacific cod
Gadus macrocephalus
blood
DNA isolation
DNA quantification
Qubit
DNA BR assay
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA Isolation and Quantification - Lake Trout Liver
DNA isolation
2024
lake trout
Salvelinus namaycush
Qubit
DNA BR assay
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Samples Received - L.staminea Histology Slides for Mac
2024
Leukoma staminea
littleneck clam
histology
slides
Samples Received
=======
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
RNA quantification
Directzol RNA miniprep
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - July 2024
2024
Daily Bits
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
RNA quantification
Directzol RNA miniprep
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-gigas-carryover
Crassostrea gigas
Pacific oyster
adult
seed
spat
Directzol RNA Miniprep
Qubit
RNA HS Assay
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
HDD RMA - Failed Gannet HDD from 20240615
gannet
HDD
Synology
=======
Samples Submitted - Littleneck Clam Histology Cassettes to UW Pathology Research Services Laboratory
2024
histology
littleneck clam
Pathology Research Services Laboratory
Samples Submitted
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-gigas-carryover
Crassostrea gigas
Pacific oyster
adult
seed
spat
Directzol RNA Miniprep
Qubit
RNA HS assay
Samples Submitted - Littleneck Clam Histology Cassettes to UW Pathology Research Services Laboratory
2024
histology
littleneck clam
Pathology Research Services Laboratory
Samples Submitted
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-gigas-carryover
Directzol RNA Miniprep
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Quantification - C.gigas RNA Lifestage Carryover from 20240615 and 20240617
2024
project-gigas-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
Qubit
RNA HS assay
=======
Computer Maintenance - Replace Bad HDD on Gannet
computer maintenance
2024
HDD
gannet
synology
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - C.gigas Lifestage Carryover Seed Juvenile and Adult
2024
project-gigas-carryover
Directzol RNA Miniprep
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
Computer Maintenance - Replace Bad HDD on Gannet
computer maintenance
2024
HDD
gannet
synology
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Differential Gene Expression - G.macrocephalus RNA-seq 9C vs 16C Using edgeR
edgeR
Pacific cod
RNA-seq
differential gene expression
2024
Gadus macrocephalus
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Samples Received - Lajonkairia lajonkairii Egg Samples from Mackenzie Gavery
Lajonkairia lajonkairii
manilla clam
2024
Samples Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - June 2024
Daily Bits
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Agarose Gel - G.macrocephalus gDNA from 20240521
agarose
gDNA
Gadus macrocephalus
Pacific cod
gel
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DNA Isolation - Pacific cod liver
DNA isolation
Pacific cod
liver
Gadus macrocephalus
DNA quantification
Qubit
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Samples Submitted - Pacific Cod 40 Tissue Samples for WGBS at Psomagen
psomagen
WGBS
2024
Pacific cod
Gadus macrocephalus
BS-seq
bisulfite
Samples Submitted
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Computer Troubleshooting - Gannet Missing Storage Pool
gannet
Synology
server
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR Analysis - C.gigas Lifestages Carryover from 20240325
2024
qPCR
Crassotrea gigas
Pacific oyster
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCRs - C.gigas Lifestage Carryover cDNA
qPCR
SsoFast
CFX Connect
HSP70
HSP90
GAPDH
VIPERIN
ATPsynthase
cGAS
DMNT1
citrate synthase
Crassostrea gigas
Pacific oyster
cDNA
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - C.gigas Lifestage Carryover Seed and Spat
RNA isolation
Crassostrea gigas
Lifestage carryover
Pacific oyster
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Reverse Transcription - C.gigas Lifestage Carryover Seed and Spat
reverse transcription
Lifestage carryover
Crassostrea gigas
Pacific oyster
cDNA
M-MLV
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
SRA Submission - CEABIGR WGBS and RNA-seq
SRA
CEABIGR
Crassostrea virginica
Eastern oyster
RNAseq
WGBS
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Resazurin - C.gigas Second Trial
Crassostrea gigas
Pacific oyster
2024
resazurin
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Resazurin - Preliminary Respiration Test Using C.gigas
resazurin
Crassostrea gigas
Pacific oyster
2024
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - Pacific cod RNA-seq Azenta Project 30-943133806
Azenta
RNA-seq
2024
Pacific cod
Gadus macrocephalus
30-943133806
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
sRNA-seq Paired Read Merging Explorations - Coral E5 Deep Dive
2024
E5
sRNA-seq
merge
bbmerge
fastp
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - February 2024
2024
Daily Bits
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Figure Updates - CEABIGR Spurious Transcription Calcs and Plotting Using Exon Sum Threshold
CEABIGR
2024
plot
Eastern oyster
Crassostrea virginica
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Exploration - CEABIGR Spurious Transcription Calculations and Plotting
2024
CEABIGR
plot
Eastern oyster
Crassostrea virginica
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Daily Bits - January 2024
2024
Daily Bits
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Computer Management - Returned Failing HDDs from Gannet Expansion Unit
computer management
2023
HDDs
gannet
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Samples Submitted - Gadus macrocephalus liver tissues to Azenta for RNA-seq
2023
Gadus macrocephalus
Pacific cod
Azenta
RNA-seq
Samples Submitted
liver
spleen
gill
blood
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Computer Maintenance - Replace Failing HDDs in Synology RX1217 Expansion Unit on Gannet
gannet
synology
RX1217
HDDs
2023
computer maintenance
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Investigation - Mysterious Case of Excessive Exons in CEABIGR
CEABIGR
Crassostrea viriginica
Eastern oyster
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Plotting Fun - Lab Meeting Task
plotting
R
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Transcriptome Annotation - M.magister De Novo Transcriptome Assembly for DuMOAR Project Using DIAMOND BLASTx on Mox
mox
DIAMOND
BLASTx
transcriptome
2023
DuMOAR
Dungeness crab
Metacarcinus magister
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Transcriptome Annotation - M.magister De Novo Transcriptome Assembly Using Trinotate on Mox
mox
2023
Metacarcinus magister
Dungenss crab
Trinotate
transcriptome
annotation
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR Analysis - C.gigas Matt George PolyIC Diploids
qPCR
CFX Connect
Crassostrea gigas
diploid
Pacific oyster
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Transcript Identification and Alignments - C.virginica RNAseq with NCBI Genome GCF_002022765.2 Using Hisat2 and Stringtie on Mox Again
hisat2
mox
Crassostrea virginica
stringtie
RNAseq
Eastern oyster
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - C.gigas PolyIC Diploid MgCl2
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Reverse Transcription - C.gigas PolyIC Diploid MgCl2
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Quantification - C.gigas PolyIC Diploid MgCl2
polyIC
Crassostrea gigas
Pacific oyster
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
sRNA-seq Alignments - E5 Coral P.evermanni Using ShortStack on Mox
sRNA
E5
Porites evermanni
ShortStack
mox
2023
E5
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Read Extractions - M.magister MEGAN FastA to FastQ Arthropoda and Unassigned Reads
Metacarcinus magister
Dungeness crab
MEGAN
2023
DuMOAR
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
DIAMOND BLASTx - C.virginica Genes on Mox
2023
CEABIGR
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - C.gigas polyIC
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Read Extractions - M.magister MEGAN Arthropoda and Unassigned Reads to FastA
Metacarcinus magister
Dungeness crab
MEGAN
2023
DuMOAR
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Quantification - C.gigas PolyIC
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Reverse Transcription - C.gigas PolyIC RNA
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - C.gigas Ctenidia cDNA for Noah’s Heat-Mechanical Stress Project
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - C.gigas Ctenidia cDNA for Noah’s Heat-Mechanical Stress Project
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - C.gigas cDNA Primer Tests for Noah’s Heat-Mechanical Stress Project
qPCR
Crassostrea gigas
cDNA
Noah
Pacific oyster
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Reverse Transcription - C.gigas RNA from Noah’s Heat-Mechanical Stress Project
reverse transcription
Crassostrea gigas
RNA
Pacific oyster
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Quantification - C.gigas RNA from Noah’s Heat-Mechanical Stress Project
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - C.gigas Ctenidia from Noah’s Heat-Mechanical Stress Project
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
File Conversion - M.magister MEGANized DAA to RMA6
megan
DAA
RMA6
Metacarcinus magister
dungeness crab
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - Pacific Cod (G.macrocephalus) Sequencing Data from Novogene
2023
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming and QC - E5 Coral sRNA-seq Data fro A.pulchra P.evermanni and P.meandrina Using FastQC flexbar and MultiQC on Mox
flexbar
E5
trimming
FastQC
MultiQC
mox
coral
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming - L.staminea RNA-seq Using FastQC fastp and MultiQC on Mox
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - P.meandrina Genome GFF to GTF Using gffread
gffread
jupyter
Pocillopora meandrina
cora
E5
GFF
GTF
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQ QC and Trimming - E5 Coral RNA-seq Data for A.pulchra P.evermanni and P.meandrina Using FastQC fastp and MultiQC on Mox
mox
FastQC
fastp
MultiQC
E5
coral
Acropora pulchra
Porites evermanni
Pocillopora meandrina
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Management - E5 Coral RNA-seq and sRNA-seq Reorganizing and Renaming
E5
coral
RNAseq
sRNAseq
2023
Data Management
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - Coral RNA-seq Data from Azenta Project 30-789513166
30-789513166
RNA-seq
Azenta
coral
Putnam
2023
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - Coral sRNA-seq Data from Azenta Project 30-852430235
2023
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
lncRNA Expression - P.generosa lncRNA Expression Using StringTie
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
lncRNA Identification - P.generosa lncRNAs using CPC2 and bedtools
lncRNA
Panopea generosa
Pacific geoduck
CPC2
bedtools
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Containers - Apptainer Explorations
apptainer
singularity
klone
mox
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Transcript Alignments - P.generosa RNA-seq Alignments for lncRNA Identification Using Hisat2 StingTie and gffcompare on Mox
gffcompare
mox
Panopea generosa
Pacific geoduck
lncRNA
StringTie
Hisat2
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQ Trimming and QC - P.generosa RNA-seq Data from 20220323 on Mox
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - Trimmed M.magister RNA-seq from NOAA
2023
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - P.verrucosa RNA-seq and WGBS Full Data from Danielle Becker
2023
E5
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - P.verrucosa v1.0 Assembly with HiSat2 on Mox
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - M.capitata HIv3 Assembly with HiSat2 on Mox
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - P.acuta HIv2 Assembly with HiSat2 on Mox
Poccillopora acuta
coral
HIv2
hisat2
mox
index
2023
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - P.verrucosa Genome GFF to GTF Using gffread
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - M.capitata Genome GFF to GTF Using gffread
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - P.acuta Genome GFF to GTF Conversion Using gffread
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - P.verrucosa NCBI GCA_014529365.1 with HiSat2 on Mox
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Genome Indexing - M.capitata NCBI GCA_006542545.1 with HiSat2 on Mox
hisat2
Montipora capitata
coral
GCA_006542545.1
mox
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
SRA Data - Coral SRA BioProject PRJNA744403 Download and QC
PRJNA744403
SRA
NCBI
fastp
FastQC
MultiQC
coral
metagenomics
2023
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Monthly Goals - January 2023
2023
Monthly Goals
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQ Trimming - Geoduck RNAseq Data Using fastp on Mox
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
FastQ Trimming and QC - C.virginica Larval BS-seq Data from Lotterhos Lab and Part of CEABIGR Project Using fastp on Mox
BSseq
Lotterhos
CEABIGR
Crassostrea virginica
Eastern oyster
fastp
mox
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - Repeat of Mussel Gill Heat Stress cDNA with Ferritin Primers
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
qPCR - Dorothys Mussel cDNA from 20220726
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation and Quantification - Dorothy Mussel Gill Samples
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
SRA Data - S.namaycush SRA BioProject PRJNA674328 Download and QC
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
SRA Submission - Ostrea lurida MBD BS-seq from 20160203
2022
SRA Submission
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Project Summary - C.virginica CEABiGR - Female vs. Male Gonad Exposed to OA
Crassostrea virginica
CEABIGR
OA
gonad
Eastern oyster
2022
Project Summary
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - Create Primary P.generosa Genome Annotation File
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - O.nerka Berdahl Brain Tissues
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Server Maintenance - Fix Server Certificate Authentication Issues
github
InCommon
certificate
servers
gannet
owl
eagle
2022
Computer Servicing
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Nextflow - Trials and Tribulations of Installing and Using NF-Core RNAseq
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - P.generosa Genomic Feature FastA Creation
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Differential Gene Expression - P.generosa DGE Between Tissues Using Nextlow NF-Core RNAseq Pipeline on Mox
nextflow
Panopea generosa
Pacific geoduck
RNAseq
nf-core
mox
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Analysis - C.virginica BSseq Unmapped Reads Using MEGAN6
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Analysis - C.virginica RNAseq Zymo ZR4059 Analyzed by ZymoResearch
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - P.generosa Genome GFF Conversion to GTF Using gffread
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Transcript Identification and Alignments - C.virginica RNAseq with NCBI Genome GCF_002022765.2 Using Hisat2 and Stringtie on Mox
hisat2
stringtie
Crassostrea virginica
Eastern oyster
RNAseq
GCF_002022765.2
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Trimming - Additional 20bp from C.virginica Gonad RNAseq with fastp on Mox
fastp
mox
Crassostrea virginica
RNAseq
trimming
Eastern oyster
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNAseq Alignment - C.virginica Adult OA Gonad Data to GCF_002022765.2 Genome Using HISAT2 on Mox
HISAT2
Crassostrea virginica
RNAseq
Mox
Eastern oyster
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Wrangling - C.virginica Gonad RNAseq Transcript Counts Per Gene Per Sample Using Ballgown
data wrangling
Crassostrea virginica
eastern oyster
R
ballgown
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Data Received - C.virginica OA Larvae DNA Methylation FastQs from Lotterhos Lab
Crassostrea virginica
Eastern oyster
larvae
DNA methylation
data received
2022
Data Received
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Project Summary - Matt George PSMFC Mytilus Byssus Project
2022
Project Summary
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - O.nerka Berdahl Brain Tissues
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - M.trossulus Gill
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - M.trossulus Gill and Phenol Gland
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - M.trossulus Gill and Phenol Gland
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - M.trossulus Gill and Phenol Gland
2022
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - M.trossulus Phenol Gland and Gill
2021
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - M.trossulus Foot and Phenol Gland
2021
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
Project Summary - O.nerka Berdahl Samples
2021
Project Summary
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9
<<<<<<< HEAD
RNA Isolation - O.nerka Berdahl Brain Tissues
2021
Miscellaneous
=======
>>>>>>> 99d1e6dabca769a2bddefd5c037c4a606dd7aaa9



















































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